Genome Biology | Volume 10 Issue 2

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

	Volume 10 Issue 2
	Comment
	Comment Many happy returns Gregory A Petsko Genome Biology 2009, 10:102 (27 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The 200th anniversary of Charles Darwin's birth is an opportunity for biologists to publicize his great idea.
	Review
	Review Sequence-based feature prediction and annotation of proteins Agnieszka S Juncker, Lars J Jensen, Andrea Pierleoni, Andreas Bernsel, Michael L Tress, Peer Bork, Gunnar von Heijne, Alfonso Valencia, Christos A Ouzounis, Rita Casadio, Søren Brunak Genome Biology 2009, 10:206 (2 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The combination of prediction tools in complex workflows and pipelines facilitates prediction of protein features from sequence.
	Review Protein function annotation by homology-based inference Yaniv Loewenstein, Domenico Raimondo, Oliver C Redfern, James Watson, Dmitrij Frishman, Michal Linial, Christine Orengo, Janet Thornton, Anna Tramontano Genome Biology 2009, 10:207 (2 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Where information on homologous proteins is available, progress is being made in automated prediction of protein function from sequence and structure.
	Minireview Epigenetic transmission of piRNAs through the female germline Sergey Shpiz, Alla Kalmykova Genome Biology 2009, 10:208 (9 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In Drosophila, piRNAs bound to Piwi proteins are transmitted to the embryo via the maternal germplasm.
	Minireview Custom astrocyte-mediated vasomotor responses to neuronal energy demand Jillian L LeMaistre, Christopher M Anderson Genome Biology 2009, 10:209 (16 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Brain astrocytes regulate local blood flow and neuronal energy supply by modulating blood vessel tone in response to changes in oxygen levels.
	Minireview Cytokinin and auxin intersection in root meristems Elisabeth J Chapman, Mark Estelle Genome Biology 2009, 10:210 (23 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Cytokinin promotes cell differentiation in plant roots by repressing auxin transport and responses at the meristem boundary.
	Minireview Reality check for malaria proteomics Robert E Sinden Genome Biology 2009, 10:211 (26 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Post-translationally modified protein isoforms are common in red blood cell stages of the malaria parasite.
	Report
	Meeting report A brave new synthetic world Farren J Isaacs, Lingchong You Genome Biology 2009, 10:302 (3 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the first meeting on 'Frontiers in Synthetic Biology', Boston, USA, 1-2 December 2008.
	Meeting report Computational biology touches all bases Susmita Datta, Somnath Datta Genome Biology 2009, 10:303 (17 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 6th Annual Rocky Mountain Bioinformatics Conference, Aspen, USA, 4-7 December 2008.
	Research
	Research Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression Fernando Faunes, Natalia Sánchez, Javier Castellanos, Ismael A Vergara, Francisco Melo, Juan Larraín Genome Biology 2009, 10:R15 (11 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of dorsal and ventral transcriptomes of Xenopus tropicalis gastrulae using serial analysis of gene expression provides at least 86 novel differentially expressed transcripts.
	Research High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research Kathrin Reichwald, Chris Lauber, Indrajit Nanda, Jeanette Kirschner, Nils Hartmann, Susanne Schories, Ulrike Gausmann, Stefan Taudien, Markus B Schilhabel, Karol Szafranski, Gernot Glöckner, Michael Schmid, Alessandro Cellerino, Manfred Schartl, Christoph Englert, Matthias Platzer Genome Biology 2009, 10:R16 (11 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genomic analysis of the annual fish Nothobranchius furzeri, a vertebrate with the shortest known life span in captivity and which may provide a new model organism for aging research.
	Research Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays Samuel P Hazen, Felix Naef, Tom Quisel, Joshua M Gendron, Huaming Chen, Joseph R Ecker, Justin O Borevitz, Steve A Kay Genome Biology 2009, 10:R17 (11 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Whole genome tiling array analysis reveals the extent of transcriptional oscillation for both coding and non-coding genes in regulating Arabidopsis thaliana circadian rhythms
	Research The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus Rachel Brower-Sinning, Donald M Carter, Corey J Crevar, Elodie Ghedin, Ted M Ross, Panayiotis V Benos Genome Biology 2009, 10:R18 (12 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RNA folding free energy is important for the evolution and host-adaptation of the influenza virus. Human virus polymerase genes are shown to have substantially higher folding free energy values than their avian counterparts.
	Research Asymmetric relationships between proteins shape genome evolution Richard A Notebaart, Philip R Kensche, Martijn A Huynen, Bas E Dutilh Genome Biology 2009, 10:R19 (12 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An investigation of metabolic networks in E. coli and S. cerevisiae reveals that asymmetric protein interactions affect gene expression, the relative effect of gene-knockouts and genome evolution.
	Research PDGF/VEGF signaling controls cell size in Drosophila David Sims, Peter Duchek, Buzz Baum Genome Biology 2009, 10:R20 (12 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Pvr and its ligands, Pvf 2 and 3, which are upstream of Ras and PI3kinase, are identified from a genome-wide screen in Drosophila cells, as regulators of cell growth.
	Research Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum Neekesh V Dharia, Amar Sidhu, María Cassera, Scott J Westenberger, Selina ER Bopp, Rich T Eastman, David Plouffe, Serge Batalov, Daniel J Park, Sarah K Volkman, Dyann F Wirth, Yingyao Zhou, David A Fidock, Elizabeth A Winzeler Genome Biology 2009, 10:R21 (13 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using tiling microarrays, a mechanism by which Plasmodium falciparum parasites acquire resistance to the antimalarial fosmidomycin has been elucidated
	Research Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes Carolina Bartolomé, Xabier Bello, Xulio Maside Genome Biology 2009, 10:R22 (18 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide comparison of transposable elements reveals evidence for unexpectedly high rates of horizontal transfer between three species of Drosophila
	Research SEPALLATA3: the 'glue' for MADS box transcription factor complex formation Richard GH Immink, Isabella AN Tonaco, Stefan de Folter, Anna Shchennikova, Aalt DJ van Dijk, Jacqueline Busscher-Lange, Jan W Borst, Gerco C Angenent Genome Biology 2009, 10:R24 (25 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A yeast 3-hybrid screen in Arabidopsis reveals MADS box protein complexes: SEP3 is shown to mediate complex formation and floral timing.
	Method Fast genomic μChIP-chip from 1,000 cells John Arne Dahl, Andrew H Reiner, Philippe Collas Genome Biology 2009, 10:R13 (10 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new method for rapid genome-wide μChIP-chip from as few as 1,000 cells.
	Software EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data Christoph Bock, Konstantin Halachev, Joachim Büch, Thomas Lengauer Genome Biology 2009, 10:R14 (10 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EpiGRAPH is a genome-scale data-mining software tool that enables users to identify epigenetic and gene regulatory features in large datasets of genomic regions.
	Software PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data Jan O Korbel, Alexej Abyzov, Xinmeng Mu, Nicholas Carriero, Philip Cayting, Zhengdong Zhang, Michael Snyder, Mark B Gerstein Genome Biology 2009, 10:R23 (23 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Paired-End Mapper (PEMer) enables mapping of genomic structural variants at considerably enhanced sensitivity, specificity and resolution over previous approaches.
	Correspondence
	Correspondence Annotations for all by all - the BioSapiens network Janet Thornton, the BioSapiens Network Genome Biology 2009, 10:401 (10 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The BioSapiens network has developed a distributed infrastructure for genome and proteome annotation by laboratories anywhere in the world.
	Correction Correction: Reactome: a knowledge base of biologic pathways and processes Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein Genome Biology 2009, 10:402 (4 February 2009) Abstract \| Full text \| PDF \| PubMed

	Volume 10 Issue 2
	Comment
	Comment Many happy returns Gregory A Petsko Genome Biology 2009, 10:102 (27 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The 200th anniversary of Charles Darwin's birth is an opportunity for biologists to publicize his great idea.
	Review
	Review Sequence-based feature prediction and annotation of proteins Agnieszka S Juncker, Lars J Jensen, Andrea Pierleoni, Andreas Bernsel, Michael L Tress, Peer Bork, Gunnar von Heijne, Alfonso Valencia, Christos A Ouzounis, Rita Casadio, Søren Brunak Genome Biology 2009, 10:206 (2 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The combination of prediction tools in complex workflows and pipelines facilitates prediction of protein features from sequence.
	Review Protein function annotation by homology-based inference Yaniv Loewenstein, Domenico Raimondo, Oliver C Redfern, James Watson, Dmitrij Frishman, Michal Linial, Christine Orengo, Janet Thornton, Anna Tramontano Genome Biology 2009, 10:207 (2 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Where information on homologous proteins is available, progress is being made in automated prediction of protein function from sequence and structure.
	Minireview Epigenetic transmission of piRNAs through the female germline Sergey Shpiz, Alla Kalmykova Genome Biology 2009, 10:208 (9 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In Drosophila, piRNAs bound to Piwi proteins are transmitted to the embryo via the maternal germplasm.
	Minireview Custom astrocyte-mediated vasomotor responses to neuronal energy demand Jillian L LeMaistre, Christopher M Anderson Genome Biology 2009, 10:209 (16 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Brain astrocytes regulate local blood flow and neuronal energy supply by modulating blood vessel tone in response to changes in oxygen levels.
	Minireview Cytokinin and auxin intersection in root meristems Elisabeth J Chapman, Mark Estelle Genome Biology 2009, 10:210 (23 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Cytokinin promotes cell differentiation in plant roots by repressing auxin transport and responses at the meristem boundary.
	Minireview Reality check for malaria proteomics Robert E Sinden Genome Biology 2009, 10:211 (26 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Post-translationally modified protein isoforms are common in red blood cell stages of the malaria parasite.
	Report
	Meeting report A brave new synthetic world Farren J Isaacs, Lingchong You Genome Biology 2009, 10:302 (3 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the first meeting on 'Frontiers in Synthetic Biology', Boston, USA, 1-2 December 2008.
	Meeting report Computational biology touches all bases Susmita Datta, Somnath Datta Genome Biology 2009, 10:303 (17 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the 6th Annual Rocky Mountain Bioinformatics Conference, Aspen, USA, 4-7 December 2008.
	Research
	Research Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression Fernando Faunes, Natalia Sánchez, Javier Castellanos, Ismael A Vergara, Francisco Melo, Juan Larraín Genome Biology 2009, 10:R15 (11 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of dorsal and ventral transcriptomes of Xenopus tropicalis gastrulae using serial analysis of gene expression provides at least 86 novel differentially expressed transcripts.
	Research High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research Kathrin Reichwald, Chris Lauber, Indrajit Nanda, Jeanette Kirschner, Nils Hartmann, Susanne Schories, Ulrike Gausmann, Stefan Taudien, Markus B Schilhabel, Karol Szafranski, Gernot Glöckner, Michael Schmid, Alessandro Cellerino, Manfred Schartl, Christoph Englert, Matthias Platzer Genome Biology 2009, 10:R16 (11 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genomic analysis of the annual fish Nothobranchius furzeri, a vertebrate with the shortest known life span in captivity and which may provide a new model organism for aging research.
	Research Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays Samuel P Hazen, Felix Naef, Tom Quisel, Joshua M Gendron, Huaming Chen, Joseph R Ecker, Justin O Borevitz, Steve A Kay Genome Biology 2009, 10:R17 (11 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Whole genome tiling array analysis reveals the extent of transcriptional oscillation for both coding and non-coding genes in regulating Arabidopsis thaliana circadian rhythms
	Research The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus Rachel Brower-Sinning, Donald M Carter, Corey J Crevar, Elodie Ghedin, Ted M Ross, Panayiotis V Benos Genome Biology 2009, 10:R18 (12 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RNA folding free energy is important for the evolution and host-adaptation of the influenza virus. Human virus polymerase genes are shown to have substantially higher folding free energy values than their avian counterparts.
	Research Asymmetric relationships between proteins shape genome evolution Richard A Notebaart, Philip R Kensche, Martijn A Huynen, Bas E Dutilh Genome Biology 2009, 10:R19 (12 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An investigation of metabolic networks in E. coli and S. cerevisiae reveals that asymmetric protein interactions affect gene expression, the relative effect of gene-knockouts and genome evolution.
	Research PDGF/VEGF signaling controls cell size in Drosophila David Sims, Peter Duchek, Buzz Baum Genome Biology 2009, 10:R20 (12 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Pvr and its ligands, Pvf 2 and 3, which are upstream of Ras and PI3kinase, are identified from a genome-wide screen in Drosophila cells, as regulators of cell growth.
	Research Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum Neekesh V Dharia, Amar Sidhu, María Cassera, Scott J Westenberger, Selina ER Bopp, Rich T Eastman, David Plouffe, Serge Batalov, Daniel J Park, Sarah K Volkman, Dyann F Wirth, Yingyao Zhou, David A Fidock, Elizabeth A Winzeler Genome Biology 2009, 10:R21 (13 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using tiling microarrays, a mechanism by which Plasmodium falciparum parasites acquire resistance to the antimalarial fosmidomycin has been elucidated
	Research Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes Carolina Bartolomé, Xabier Bello, Xulio Maside Genome Biology 2009, 10:R22 (18 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A genome-wide comparison of transposable elements reveals evidence for unexpectedly high rates of horizontal transfer between three species of Drosophila
	Research SEPALLATA3: the 'glue' for MADS box transcription factor complex formation Richard GH Immink, Isabella AN Tonaco, Stefan de Folter, Anna Shchennikova, Aalt DJ van Dijk, Jacqueline Busscher-Lange, Jan W Borst, Gerco C Angenent Genome Biology 2009, 10:R24 (25 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A yeast 3-hybrid screen in Arabidopsis reveals MADS box protein complexes: SEP3 is shown to mediate complex formation and floral timing.
	Method Fast genomic μChIP-chip from 1,000 cells John Arne Dahl, Andrew H Reiner, Philippe Collas Genome Biology 2009, 10:R13 (10 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new method for rapid genome-wide μChIP-chip from as few as 1,000 cells.
	Software EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data Christoph Bock, Konstantin Halachev, Joachim Büch, Thomas Lengauer Genome Biology 2009, 10:R14 (10 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EpiGRAPH is a genome-scale data-mining software tool that enables users to identify epigenetic and gene regulatory features in large datasets of genomic regions.
	Software PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data Jan O Korbel, Alexej Abyzov, Xinmeng Mu, Nicholas Carriero, Philip Cayting, Zhengdong Zhang, Michael Snyder, Mark B Gerstein Genome Biology 2009, 10:R23 (23 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Paired-End Mapper (PEMer) enables mapping of genomic structural variants at considerably enhanced sensitivity, specificity and resolution over previous approaches.
	Correspondence
	Correspondence Annotations for all by all - the BioSapiens network Janet Thornton, the BioSapiens Network Genome Biology 2009, 10:401 (10 February 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The BioSapiens network has developed a distributed infrastructure for genome and proteome annotation by laboratories anywhere in the world.
	Correction Correction: Reactome: a knowledge base of biologic pathways and processes Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein Genome Biology 2009, 10:402 (4 February 2009) Abstract \| Full text \| PDF \| PubMed

Explore Genome Biology

Articles

Volume 10 Issue 2

Comment

Review

Report

Research

Correspondence